Related papers: Biological Organization and Negative Entropy: Base…
The emergence of life from inanimate matter presents a thermodynamic challenge: the Second Law of Thermodynamics dictates a global trend towards disorder, yet life constitutes localized pockets of profound organization. This paper presents…
This letter seeks to illuminate the profound connection between complexity, self-organization, emergent behaviour, pattern formation, and entropy concepts that are foundational to understanding our universe. By examining these ideas through…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Living systems are thermodynamically open but closed in their organization. In other words, even though their material components turn over constantly, a material-independent property persists, which we call organization. Moreover,…
Active biological systems reside far from equilibrium, dissipating heat even in their steady state, thus requiring an extension of conventional equilibrium thermodynamics and statistical mechanics. In this Letter, we have extended the…
There are three ways to conceptualize entropy: entropy as an extensive thermodynamic quantity of physical systems (Clausius, Boltzmann, Gibbs), entropy as a measure for information production of ergodic sources (Shannon), and entropy as a…
The idea is advanced that self-organization in complex systems can be treated as decision making (as it is performed by humans) and, vice versa, decision making is nothing but a kind of self-organization in the decision maker nervous…
A new method to deal with reduced dynamics of open systems by means of the Schr\"odinger equation is presented. It allows one to consider the reduced time evolution for correlated and uncorrelated initial conditions.
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Schroedinger's book 'What is Life?' is widely credited for having played a crucial role in development of molecular and cellular biology. My essay revisits the issues raised by this book from the modern perspective of epigenetics and…
Aging is a universal consequence of life, yet researchers have identified no universal theme. This manuscript considers aging from the perspective of entropy, wherein things fall apart. We first examine biological information change as a…
A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The…
Physics relies on mathematical spaces carefully matched to the phenomena under study. Phase space in classical mechanics, Hilbert space in quantum theory, configuration spaces in field theory all provide representations in which physical…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
Many problems in evolutionary theory are cast in dyadic terms, such as the polar oppositions of organism and environment. We argue that a triadic conceptual structure offers an alternative perspective under which the information generating…
There is a widespread assumption that the universe in general, and the Earth's biosphere in particular, is becoming more complex over time. This paper formulates this assumption as a macroscopic law, the law of increasing complexity, for a…
The science of thermodynamics was put together in the Nineteenth Century to describe large systems in equilibrium. One part of thermodynamics defines entropy for equilibrium systems and demands an ever-increasing entropy for non-equilibrium…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
The possibility of a fundamental consistency between the basic quantum principles and reduction (so-called wave function reduction) is reexamined. The mathematical description of an organized macroscopic device is constructed explicitly as…